On 15 May 1710, King João V of Portugal appointed him dean of the Royal Chapel, which had recently been built as a collegiate church of São Tomé on 1 March of that year.

On 7 November 1716, the Royal Chapel became a patriarchal metropolitan See by the papal bull In supremo apostolatus and José Manuel became a member of the Sacred College of Principals, and as its rector, he presided over the Te Deum, in which for the first time all the dignities used habits of prelate.

[1] Assigned as a judge of the Supreme Court of the Inquisition of Lisbon, and president of the Great Curia.

He took office on 2 June and was consecrated on 25 July in Lisbon by Cardinal Lucas Melchor Tempi, titular archbishop of Nicomedia, apostolic nuncio to Portugal, assisted by Jose Henriques, bishop of Constantine, and Hilário of Santa Rosa, ex-bishop of Macau.

The funeral took place on 12 July, in the Mother Church of Our Lady of the Assumption of Atalaia, where he was buried in the side wall of the main chapel.